Clarke Labs

Published Data In Robert Clarke Laboratory

Ellis et al. Clin Cancer Res 8: 1155-1166, 2002

Overview

Fulltext

Protocol

Table1

Table2

3D PCA

Dendrogram

Images

Development and Validation of a Method for Using Breast Core Needle Biopsiesfor Gene Expression Microarray Analyses." Ellis et al., Clin Cancer Res 8: 1155-1166, 2002.

Overview

We have developed an optimal tissue acquisition, processing, and analysis procedures for exploring the gene expression profiles of breast core needle biopsies representing cancer and noncancer tissues. Processing tissue through RNA Later TM (download information on RNA Later from Ambion) preserves tissue architecture if biopsies are washed for 5 min on ice with ice-cold phosphate buffered saline prior to histopathologic analysis. Adequate concentrations of high quality RNA are recovered for gene expression microarray analysis. Molecular profiles from biopsies processed through RNA Later TM are similar to those from snap frozen tissues. These profiles were used to build a neural network classifier that accurately discriminates between predominantly cancer and noncancer breast biopsies.

Links to Paper and Data

Link to Paper (at Clinical Cancer Research Web Site)
Tissue acquisition and processing protocol (adapted from Figure 4 in paper)
Table of Top 30 Genes (adapted from Table 4 in paper)
Table of Top 103 Genes (not in paper)
Rotating 3D Projection of Top 103 Dimensions (not in paper)
Hierarchical Clustering Based on Top 103 Dimensions (not in paper)
Color Figures (adapted from Figures 2 & 3 in paper) - graphics